RetrogeneDB ID: retro_cjac_2312

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:17879288..17879633(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AP1S2
• Ensembl ID: ENSCJAG00000004393
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 2 subunit [Source:HGNC Symbol;Acc:560]

Sequence

>retro_cjac_2312
AAAAAGATCACCAGAGAACTTGTTCAGACCATTTTAGCACGGAAACCTAAAATGTGCAGCTTCCTTGAGTGGCGAGATCT
GAAGATTGTTTACAAAAGATATGCTAGTCTGTAGTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGG
AAATAATTCATCGTTACGTGGAATTACTTGACAAGTATTTTGTCAGTGTCTGTGAACTAGATATCATCTTTAATTTTGAG
AAGGCTTATTTTATTTTGGATGAGTTTCTTTTGGGAGGGGAAGTTCAGGAAACATCCAAGAAAAATGTCCTTAAAGCAAT
TGAGCAGGCCGATCTACTGCAGGAG

Alignment

ORF - retro_cjac_2312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.39 %
• Parental protein coverage: 73.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAIEDQDNELITLEIIHRYVELLDKYFGSV
          KKITRELVQT.LARKPKMCSFLEWRDLKIVYKRYASL.FCCAIEDQDNELITLEIIHRYVELLDKYF.SV
Retrocopy KKITRELVQTILARKPKMCSFLEWRDLKIVYKRYASL*FCCAIEDQDNELITLEIIHRYVELLDKYFVSV

Parental  CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE
          CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE
Retrocopy CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.27 RPM	12.56 RPM
SRP051959_heart	0.54 RPM	18.86 RPM
SRP051959_kidney	0.16 RPM	12.82 RPM
SRP051959_liver	0.24 RPM	7.67 RPM
SRP051959_lung	0.60 RPM	28.61 RPM
SRP051959_lymph_node	0.46 RPM	23.26 RPM
SRP051959_skeletal_muscle	0.28 RPM	5.70 RPM
SRP051959_spleen	0.80 RPM	50.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2312 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020420	1 retrocopy	retro_btau_1308,
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312 ,
Callithrix jacchus	ENSCJAG00000005786	1 retrocopy	retro_cjac_2742,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Homo sapiens	ENSG00000182287	1 retrocopy	retro_hsap_1849,
Macaca mulatta	ENSMMUG00000014055	1 retrocopy	retro_mmul_1716,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386,
Pteropus vampyrus	ENSPVAG00000010218	1 retrocopy	retro_pvam_783,
Sorex araneus	ENSSARG00000000117	1 retrocopy	retro_sara_575,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Sus scrofa	ENSSSCG00000012142	1 retrocopy	retro_sscr_998,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,
Tupaia belangeri	ENSTBEG00000008834	2 retrocopies	retro_tbel_2173, retro_tbel_4575,
Tarsius syrichta	ENSTSYG00000005290	2 retrocopies	retro_tsyr_1953, retro_tsyr_854,
Vicugna pacos	ENSVPAG00000007642	1 retrocopy	retro_vpac_596,